Re: [phenixbb] refine double conformations of a glycan

22 Feb 2012

      Could you try this?

  apply_cif_link {
    data_link = "NAG-ASN"
    residue_selection_1 = chain A and resname NAG and resid 2061
    residue_selection_2 = chain A and resname ASN and resid 61
  }

I hope this works for both conformers.
Off the top of my head I'm not sure anymore how exactly we handle the
conformers. If the above doesn't work insert "and altloc A", with a copy
for "and altloc B", similar to what you tried.

Ralf

On Tue, Feb 21, 2012 at 5:15 PM, Qiang Chen wrote:
...
Hi all,
In my structure, the ASN and the linked NAG has two conformations. The pdb:
ATOM   3685  C1 ANAG A2061       4.069   2.862  24.649  0.47 31.33
 C
ANISOU 3685  C1 ANAG A2061     3426   4664   3813   -664    421    625
 C
ATOM   3686  C1 BNAG A2061       9.105   0.384  22.719  0.53 40.81
 C
ANISOU 3686  C1 BNAG A2061     5087   5333   5084     24    -72   -116
 C
ATOM   3690  C2 ANAG A2061       4.508   1.905  25.749  0.47 34.38
 C
ANISOU 3690  C2 ANAG A2061     3953   4727   4383   -441    142    473
 C
ATOM   3691  C2 BNAG A2061       8.311  -0.893  22.808  0.53 40.91
 C
ANISOU 3691  C2 BNAG A2061     5087   5438   5018     13    -55    -37
 C
ATOM   3694  N2 ANAG A2061       5.010   0.727  25.059  0.47 35.56
 N
ANISOU 3694  N2 ANAG A2061     4185   4888   4437   -466    149    254
 N
ATOM   3695  N2 BNAG A2061       7.220  -0.767  23.761  0.53 40.82
 N
ANISOU 3695  N2 BNAG A2061     5159   5512   4836    246   -144   -112
 N
ATOM   3698  C7 ANAG A2061       6.312   0.507  24.874  0.47 34.61
 C
ANISOU 3698  C7 ANAG A2061     4357   4653   4141   -406    202    282
 C
ATOM   3699  C7 BNAG A2061       5.974  -1.172  23.460  0.53 41.98
 C
ANISOU 3699  C7 BNAG A2061     5327   5677   4943    117      8   -149
 C
ATOM   3700  O7 ANAG A2061       7.194   1.236  25.322  0.47 35.05
 O
ANISOU 3700  O7 ANAG A2061     4292   4626   4396   -724    290    343
 O
ATOM   3701  O7 BNAG A2061       5.625  -1.665  22.371  0.53 44.02
 O
ANISOU 3701  O7 BNAG A2061     5616   5774   5335      6   -122   -208
 O
ATOM   3702  C8 ANAG A2061       6.699  -0.698  24.067  0.47 33.30
 C
ANISOU 3702  C8 ANAG A2061     4119   4700   3832   -193     57    303
 C
ATOM   3703  C8 BNAG A2061       4.933  -0.984  24.514  0.53 42.31
 C
ANISOU 3703  C8 BNAG A2061     5260   5612   5203    157     -4   -125
 C
ATOM   3710  C3 ANAG A2061       3.357   1.608  26.717  0.47 34.94
 C
ANISOU 3710  C3 ANAG A2061     3903   4950   4420   -528    289    456
 C
ATOM   3711  C3 BNAG A2061       9.296  -2.001  23.171  0.53 40.83
 C
ANISOU 3711  C3 BNAG A2061     5144   5347   5021     31   -211    -83
 C
ATOM   3714  O3 ANAG A2061       3.801   0.844  27.813  0.47 37.07
 O
ANISOU 3714  O3 ANAG A2061     4043   5387   4655   -327    106    508
 O
ATOM   3715  O3 BNAG A2061       8.608  -3.231  23.147  0.53 41.68
 O
ANISOU 3715  O3 BNAG A2061     5286   5504   5046   -142   -263     97
 O
ATOM   3718  C4 ANAG A2061       2.696   2.880  27.229  0.47 33.38
 C
ANISOU 3718  C4 ANAG A2061     3490   4870   4323   -715    378    575
 C
ATOM   3719  C4 BNAG A2061      10.480  -2.021  22.187  0.53 39.61
 C
ANISOU 3719  C4 BNAG A2061     4854   5338   4854     85   -226    -13
 C
ATOM   3722  O4 ANAG A2061       1.507   2.534  27.956  0.47 35.04
 O
ANISOU 3722  O4 ANAG A2061     3669   4878   4766   -843    393    668
 O
ATOM   3723  O4 BNAG A2061      11.583  -2.708  22.745  0.53 37.22
 O
ANISOU 3723  O4 BNAG A2061     4397   5524   4220    146   -644     59
 O
ATOM   3726  C5 ANAG A2061       2.336   3.744  26.026  0.47 34.15
 C
ANISOU 3726  C5 ANAG A2061     3749   4890   4334   -733    503    550
 C
ATOM   3727  C5 BNAG A2061      11.003  -0.643  21.780  0.53 39.23
 C
ANISOU 3727  C5 BNAG A2061     4886   5258   4760     33   -165    -30
 C
ATOM   3730  C6 ANAG A2061       1.625   5.025  26.471  0.47 35.40
 C
ANISOU 3730  C6 ANAG A2061     4140   4847   4461   -657    269    378
 C
ATOM   3731  C6 BNAG A2061      11.764  -0.744  20.462  0.53 39.76
 C
ANISOU 3731  C6 BNAG A2061     5000   5228   4877     79   -185   -106
 C
ATOM   3736  O6 ANAG A2061       2.432   5.674  27.428  0.47 37.10
 O
ANISOU 3736  O6 ANAG A2061     4302   5083   4710   -773    428    205
 O
ATOM   3737  O6 BNAG A2061      10.918  -1.227  19.435  0.53 40.11
 O
ANISOU 3737  O6 BNAG A2061     4599   5472   5169    313    -83   -277
 O
ATOM   3740  O5 ANAG A2061       3.507   4.032  25.210  0.47 33.36
 O
ANISOU 3740  O5 ANAG A2061     3905   4796   3974   -742    445    909
 O
ATOM   3741  O5 BNAG A2061       9.974   0.304  21.624  0.53 39.18
 O
ANISOU 3741  O5 BNAG A2061     5023   5184   4676   -220    -99   -108
 O
ATOM   1157  N   ASN A  61       8.496   4.626  20.319  1.00 26.85
 N
ANISOU 1157  N   ASN A  61     3029   4695   2476  -1809   -655   1273
 N
ATOM   1158  CA AASN A  61       7.080   4.398  20.655  0.50 24.65
 C
ANISOU 1158  CA AASN A  61     2996   4000   2368  -1776   -634    980
 C
ATOM   1159  CA BASN A  61       7.083   4.446  20.752  0.50 25.61
 C
ANISOU 1159  CA BASN A  61     3174   4178   2376  -1622   -618    912
 C
ATOM   1162  CB AASN A  61       6.952   3.807  22.077  0.50 23.96
 C
ANISOU 1162  CB AASN A  61     2901   3704   2497  -1862   -440   1083
 C
ATOM   1163  CB BASN A  61       7.016   4.118  22.260  0.50 26.04
 C
ANISOU 1163  CB BASN A  61     3226   4291   2376  -1605   -554    824
 C
ATOM   1168  CG AASN A  61       5.499   3.653  22.494  0.50 27.33
 C
ANISOU 1168  CG AASN A  61     3048   4420   2914  -1388   -585    598
 C
ATOM   1169  CG BASN A  61       7.882   2.975  22.608  0.50 27.64
 C
ANISOU 1169  CG BASN A  61     3195   4695   2612  -1576   -444    650
 C
ATOM   1170  OD1AASN A  61       4.659   3.204  21.697  0.50 27.73
 O
ANISOU 1170  OD1AASN A  61     3349   4200   2986  -1314   -644    873
 O
ATOM   1171  OD1BASN A  61       8.908   3.141  23.291  0.50 30.84
 O
ANISOU 1171  OD1BASN A  61     3734   4991   2990  -1345   -880    129
 O
ATOM   1172  ND2AASN A  61       5.182   4.096  23.716  0.50 34.27
 N
ANISOU 1172  ND2AASN A  61     3736   5474   3811   -832   -539    234
 N
ATOM   1173  ND2BASN A  61       7.512   1.797  22.152  0.50 34.10
 N
ANISOU 1173  ND2BASN A  61     5062   4644   3251  -1031   -186    246
 N
I put link in .def file like this:
  apply_cif_link {
    data_link = "NAG-ASN"
    residue_selection_1 = chain A and resname ANAG and resid 2061
    residue_selection_2 = chain A and resname AASN and resid 61
  }
  apply_cif_link {
    data_link = "NAG-ASN"
    residue_selection_1 = chain A and resname BNAG and resid 2061
    residue_selection_2 = chain A and resname BASN and resid 61
  }
but when I run the .def file, I got an error message:
couldn't find :residue_selection_1 = chain A and resname ANAG and resid
2061
Is there any wrong in my file?
Thank you very much!
yamei
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Re: [phenixbb] refine double conformations of a glycan

Ralf Grosse-Kunstleve